General Overview

This repository provides scripts to calibrate the Atlantis ecosystem model using the calibrar R package.
The example included here is applied to the Puget Sound Atlantis configuration.

Folder structure

R scripts

• runModel_Atlantis.R
  Wrapper function used by calibrar to run the Atlantis model with a new set of parameters. This script launches the model simulation and extracts the model outputs required for the calibration process.

• calibrate_MPI.R
  Main script used to run the calibration procedure using the calibrar package. It loads all the calibration settings, parameters to estimate, and launches the optimization routine.

CSV files

• calibration_settings.csv
  Configuration file defining targets location and setup.

• calibration-parameters-complete.csv
  Table listing the calibrated Atlantis parameters with their initial values and bounds.

Folders

• configuration
  Contains the Atlantis configuration.

• data
  Calibration targets.

• keep_track_calibration
  Stores the outputs of each automated calibration trial with calibrar. Scripts to explore the outputs of calibrar are available.

• create_Atlantis_calibrar_files
  Scripts used to generate the input files required by calibrar, including formatted parameter tables and calibration configuration files. We recommand to use them as example only if needed. These script are quite basic.

Recommendations for performing an Atlantis calibration with calibrar

To perform the Atlantis Calibration with calibrar, review our material in this order:

1. Read our preprint describing the calibration of Atlantis using calibrar:
   https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5888414

2. Go through the slides presenting the article:
   https://docs.google.com/presentation/d/1LF5dIWs0NObyVicStsMRFs5jmnmBjcYI/edit

3. Watch the recording of the workshop describing the files and scripts:
   https://drive.google.com/file/d/1QSdkpcLq7TR39WiESiUJAEdU-YdxBp5o/view

   A transcript of the workshop is also available:
   https://docs.google.com/document/d/1vbCfxM_akezcLdmvxRtgcGKmWH44Ju6m/edit

4. Pull and explore the code for the packages linking Atlantis and calibrar:

   • https://github.com/alaiam/Atlantis_Calibration
   • https://github.com/alaiam/atlantis2ls

5. Explore the calibrar package and associated publication:
   https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.14452